I started working out on Tuesday and today is my second workout. I did squats on Tuesday and today my legs are still so sore I have trouble going from standing to sitting, sitting to standing, and stairs are just mean and nasty. Should I still do squats today or skip them? I am not injured, its not that kind of pain, but I am VERY sore. To add to my question what causes this kind of soreness and is there anything that can be done to minimize it or shorten the recovery?

Your body is telling you no more but a trick is to lower the weight by 40 pounds and do your squats. it will make you feel better trust me. It will pump blood to your muscles helping them recover.
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DFG4Aug 18 '11 at 15:45

Adding to/agreeing with DFG4 - If I force myself to do weight training despite soreness, I often feel less sore at the end of the workout than I did at the beginning. Just lower the weight and take it easy, but do your workout anyway. Did you start with just the bar on Tuesday? If so, skip the bar today and just do bodyweight squats. Or, if you're already putting more than 50 pounds on the bar, take 40-50 pounds off and try it that way. Then add 5 pounds per work out until you get back to where you were.
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Joshua CarmodyAug 18 '11 at 17:43

2 Answers
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The short answer is yes continue your normally scheduled workout session. The soreness will be greatly lessened over time as you get used to using your muscles regularly. It is better to have a light day and keep exercising than it is to skip altogether.

Now, severe DOMS (delayed onset muscle soreness), as it sounds like you are experiencing, is a symptom of asking your unadapted body to do a lot more work than it was ready for. The problem is not strength, but fatigue and recovery. Your body isn't used to bouncing back from doing hard work yet.

My recommendation for you is to:

Deload about 20% (reduce the weight on the bar), and concentrate on form. You want to go to at least parallel to get the most from the exercise. If you can't do the exercise with proper form, keep taking weight off until you can. Bad technique is what causes injuries.

Use that new lower weight as your current work weight and progressively load from there (add 5 lbs or 2.5kg per session).

Use a foam roller and stretch after you exercise. This will help aid in recovery.

Let's say for example, you jumped in your first session with 135lb squats and you are not accustomed to that type of exercise. You would deload to 105lb and work up from there. Now, let's say when you did the 135lb squats you only went halfway down. The weight was too heavy for you then and it's too heavy for you now. You might have to go all the way down to 65lb or even the empty bar to get the technique right. When you are starting out, technique is more important than the weight on the bar.

Muscle soreness is caused by damage to your muscles from your workout. This is a good thing, as it tells your muscles to adapt. As long as you are differentiating between soreness and injury, you can work out while sore. In fact, working out the same muscles will probably reduce the soreness you are feeling. Once you warm up, you might find the majority of your pain has dissipated.

One thing you can do on your off days to reduce soreness is active recovery. This involves light exercise that increases blood flow. Just walking or cycling slowly are examples that would help with your leg soreness.

Finally, you can use ice to reduce inflammation, reduce pain, and speed up the recovery process.